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See the list of commands here.
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The standard syntax of Rasmol select command can be used in Friend. Additionaly the syntax of the command is extended to allow selection of particular molecule:
select @molecule_index [sel_expr]
Molecules are indexed incrementally starting from zero in the order they have been loaded, i.e. first loaded molecule will have index 0. sel_expr is the standard Rasmol selection expression.
Examples:
select @0 *.CA
select @0 water
select @1 ala
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This command allows you to load structure into the program by PDB-code. The usage is as follows:
pload pdbcode
The file for specified PDB-code will be downloaded from mirror PDB site at mozart.bio.neu.edu, saved into local cache, and loaded into program. Next time a user applies the command to the same PDB-code Friend will be automatically retriev corresponding file from the cache. The first chain in PDB-file will be shown in sequence alignment window. To display a different chain a user can specify chain as follows (no '|' should be put in real command):
pload pdbcode|chain
Examples:
pload 1qdl
pload 1qdlB
pload 1bxrC
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This commands allows you to display successively multiple, i.e. NMR, conformations of a structures. All conformations have to be loaded from one file. To use the command mark only one sequence in sequence alignment window and type:
movie [delay] [n_loops]
where delay is delay between showing successive conformations (measured in miliseconds), and n_loops is number of times the movie has to be replayed. Both parameters are optional. The default values are 33 and 1 respectively.
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